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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription dependent dynamic supercoiling in Raji human B cells in vivo

ABSTRACT: Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation. Raji cells: untreated and treated with DRB, CPT and BLAP. Three biological replicates per treatment, each hybridized to new array. Total: 12 samples (4 treatments x 3 replicates).

ORGANISM(S): Homo sapiens

SUBMITTER: Damian Wojtowicz

PROVIDER: E-GEOD-43751 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription dependent dynamic supercoiling in Raji human B cells in vivo

Project description:Transcription has the capacity to modify mechanically DNA topology, DNA structure, and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn, may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dynamics, we charted an ENCODE map of transcription-dependent dynamic supercoiling in human Burkitt lymphoma cells using psoralen photobinding to probe DNA topology in vivo. Dynamic supercoils spread ~1.5 kb upstream of the start sites of active genes. Low and high output promoters handle this torsional stress differently as shown using inhibitors of transcription and topoisomerases, and by chromatin immunoprecipation of RNA polymerase and topoisomerases I and II. Whereas lower outputs are managed adequately by topoisomerase I, high output promoters additionally require topoisomerase II. The genome-wide coupling between transcription and DNA topology emphasizes the importance of dynamic supercoiling for gene regulation.

2013-02-16 | GSE43751 | GEO

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [NimbleGen ChIP-chip]

Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, M-bM-^@M-^\openM-bM-^@M-^] chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. The binding of bTMP, as a reporter for DNA supercoiling, was investigated in RPE1 cells. Experiments were biological replicates

2013-02-17 | E-GEOD-43448 | biostudies-arrayexpress

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Agilent ChIP-chip]

2013-02-17 | E-GEOD-43450 | biostudies-arrayexpress

RNA Polymerase-II-generated DNA supercoils destabilize nucleosomes

Project description:The twin supercoiled domain model posits that, as RNA Polymerase II (Pol II) transcribes a gene, it generates negative and positive supercoils upstream and downstream respectively, but little is known about the functional consequence in vivo of the resulting torsional strain. Here we provide a method for high resolution mapping of DNA supercoils using next-generation sequencing, and show that the level of supercoiling is correlated with gene expression in Drosophila cells. Inhibition of topoisomerases, enzymes that relieve torsional strain, leads to accumulation of supercoils surrounding gene bodies and of Pol II at the transcription start sites. Topoisomerase I inhibition results in increased nascent RNA transcripts with Topoisomerase II inhibition shows little change in nascent RNA levels. Despite these different effects on transcription, inhibition of either enzyme results in increased nucleosome turnover within gene bodies, suggesting that torsional stress contributes to destabilizing nucleosomes ahead of Pol II. 12 paired-end samples and 8 single-end samples were sequenced and analyzed.

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Chromatin immunoprecipitation of fission yeast to identify topoisomerase I and II activity

Project description:Eukaryotic topoisomerase I and II relax DNA and are key components in the processes of DNA replication, transcription and genome stability. It is not clear, however, how their activity controls epigenetic states across an entire eukaryotic genome. Using the fission yeast model Schizosaccharomyces pombe, we investigate genome-wide how topoisomerases affect chromatin formation through nucleosome occupancy and regulate transcription. We show that topoisomerase activity is required for nucleosome turnover at promoter regions, affecting epigenetic gene regulatory states, and for effective termination of transcription.

2010-07-02 | E-MEXP-1850 | biostudies-arrayexpress

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Illumina transcription]

Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, M-bM-^@M-^\openM-bM-^@M-^] chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. The gene transcription of 3 independent biological replicates were investigated

2013-02-17 | E-GEOD-43449 | biostudies-arrayexpress

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase

Project description:Genome-wide distribution of topoisomerase I and DNA gyrase is directed by transcription induced supercoiling

2017-01-31 | GSE85357 | GEO

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Agilent ChIP-chip]

Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes.

2013-02-17 | GSE43450 | GEO

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Illumina transcription]

Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes.

2013-02-17 | GSE43449 | GEO

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [NimbleGen ChIP-chip]

Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes.

2013-02-17 | GSE43448 | GEO

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